Metabolite profiling for plant functional genomics

Oliver Fiehn, Joachim Kopka, Peter Dörmann, Thomas Altmann, Richard N. Trethewey, Lothar Willmitzer

Research output: Contribution to journalArticlepeer-review

1667 Scopus citations


Multiparallel analyses of mRNA and proteins are central to today's functional genomics initiatives. We describe here the use of metabolite profiling as a new tool for a comparative display of gene function. It has the potential not only to provide deeper insight into complex regulatory processes but also to determine phenotype directly. Using gas chromatography/mass spectrometry (GC/MS), we automatically quantified 326 distinct compounds from Arabidopsis thaliana leaf extracts. It was possible to assign a chemical structure to approximately half of these compounds. Comparison of four Arabidopsis genotypes (two homozygous ecotypes and a mutant of each ecotype) showed that each genotype possesses a distinct metabolic profile. Data mining tools such as principal component analysis enabled the assignment of 'metabolic phenotypes' using these large data sets. The metabolic phenotypes of the two ecotypes were more divergent than were the metabolic phenotypes of the single-loci mutant and their parental ecotypes. These results demonstrate the use of metabolite profiling as a tool to significantly extend and enhance the power of existing functional genomics approaches.

Original languageEnglish (US)
Pages (from-to)1157-1161
Number of pages5
JournalNature Biotechnology
Issue number11
StatePublished - 2000
Externally publishedYes


  • Arabidopsis thaliana
  • Bioinformatics
  • Cluster analysis
  • Functional genomics
  • Metabolite profiling
  • Metabolomics

ASJC Scopus subject areas

  • Microbiology


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